Shinobi Hero
by RougeOne
Summary: Saving his city, helping villains it's all in a day's work for Naruto in this strange new world. Too bad it puts him on the bad sides of the Justice Leauge.
1. Chapter 1

Disclaimer: I Do Not Own Naruto Or DC

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(Justice League Headquarters)

Orbiting Planet Earth a billion dollar space station, home to a variety of heroes, human and alien alike held a very somber mood. Gathered together in one of the stations many conference rooms five of the founding members of the Justice League stared at the newswoman reporting another villain's death at the hands of the New York City vigilante. "Witness say the Villain FireFly attacked down the street from where I'm standing now. Just weeks ago this same man was arrested in Gotham after being defeated by the Batman and once again escaped imprisonment after being transferred to the new state of the art Prison here in NYC. And once more, an escaped villain falls at the hands of our very own Hero. The Government is at odds with the people as many can't find it in them to care about the death of a madman. Many believe and I quote that _"It's about time someone stopped these guys from running loose."_ This is Amy Satran on channel eight signing off."

"Can you believe this madness. A whole city, rallying behind a murderer." Clark Kent aka Superman said glaring at the television. Heroes put away killers they weren't them. "This man is no hero; he's a vigilante a murderer."

Unanimous nods went around the table, Batman, Green Lantern, the Flash, Aquaman and Wonder Woman all agreeing with their Kryptonian friend. They defeated and caught criminals, but the Justice system decided what the punishment for the crime was. That was how the world stayed in order and didn't dissolve into chaos. When one murderer was allowed to kill then, the rest would think they had the same right.

"Have you got any leads on him, Batman?" asked Hal Jordan aka Green Lantern. He had killed before in the line of duty and understood that sometimes that was the only way. But whoever this Vigilante was killed because he decided alone that his victims didn't deserve to live.

Shaking his head Bruce Wayne aka Batman scowled at the monitor. He had reached out to some contacts in New York, but miss Satran had been correct when she said no one there wanted the city's 'Hero' to be caught. "I found one person of interest; a 17-year-old Naruto Uzumaki moved to New York about a year ago, the same time as the Vigilante started showing up."

"Surely you don't think a child would be able to do this?" Barry Allen aka the Flash had always respected Batman for being an average human and fighting off super powered beings, but sometimes the man's paranoia was a lot to handle.

"Flash is correct I do not think a mere boy would be capable of murdering our enemies." Diana Prince aka Wonder Woman spoke up for the first time. Her island had told stories of the land of man and while some turned out to be true others didn't. Along her way to becoming the hero she was today she had to find her own beliefs and a murdering, child was not something she could believe.

"I didn't say it was him, I had him watched and when he was home, or even in public the vigilante was spotted so it couldn't have been him."-glaring at the group Batman stood cape billowing-"I'm heading back to the cave to see if I can find anything else."

With Batman's departure, the meeting closed all heroes heading back their respected city each having the same thought. If they did catch the New York Vigilante would he be prosecuted or let loose to stop more villains permanently?

(New York City, City Hall)

"I would like to thank you all for coming." Naruto Uzumaki said face hidden behind a fox style ANBU mask. In front of him seated in their chairs at city all the New York Mayor of New York and the Mayor-council nodded politely to the Hero.

"It is of no consequence, but you must understand that this meeting can not go public." The Mayor said.

"Of course Mr. Mayor. The leaders of New York meeting with a murderer without having him arrested. Quite the scandal." Naruto got a few chuckles from the younger members of the council but, the older and wiser ones frowned at his lack of professionality. Straightening up Naruto tossed a folder onto the table in front of the Mayor. "Do you know who that is?"

"Of course we do, she is one of Gotham's Villains, currently residing in Arkham Asylum." One of the council women spoke reading through the folder as Naruto passed more copies out.

"Not for long."

"You think she is going to escape?" The Mayor asked.

Shaking his head Naruto pulled more folders from his cloak handing them out to the council. "No, I would like her transferred here to New York."

"We won't be accomplices to the murders of villains, No matter how cruel they are." Each of the council members nodded along in agreement.

Sighing underneath his mask, Naruto cursed the stupidity of councils. It seemed no matter what world he was in he couldn't escape from them. "I do not wish to kill her I would like to have her rehabilitated."

"Rehabilitate a villain. Are you out of your mind!"

"No, she didn't decide to become a villain she was forced. How long do any of you think you could have lasted before breaking like she did." Naruto questioned angrily. "If anyone of the other heroes had half a brain or anyone in Gotham could think straight they would see she doesn't need jail time; she needs help. Now are one of you going to do the right thing and sign the transfer slips?"

(Gotham City, Arkham Asylum)

"Ooh, look red it's the boys in blue. You boys here to let me go?" Harleen Quinzel aka Harley Quinn asked pouting cutely at the guards outside her cell. "Oh come on, don't ignore me."

"Let it go, Harley. No one working her falls for your tricks anymore."

Glaring at through at Poison Ivy who was in her own cell Harley stuck her tongue out at the plant villain. "Just you wait red; Imma gets outta here soon."

"Todays your lucky day then Ms. Quinn you are being transferred." One of the cops said sliding a pair of handcuffs through the food vent. "Put those on please."

"Ms. Quinn and please." Harley laughed putting on the cuffs. "What do you think red he must not be from Gotham."

"No, I don't think so." Ivy grin dropped as the cops waiting to take Harley away smiled. "What are you idiots smiling for?"

"You never let us tell you where Ms. Quinn is being transferred to." The cop who handed the handcuffs to the blonde said smiling even wider. "The reason we are so polite today Ms. Quinn is that you should always have respect for the dead."

"Dead?" Harley asked confused. "What you three planning on busting me out then offing me?"

"We aren't going to kill you, just send you to New York."

"New York!" Harley screamed as Ivy gasped. New York wasn't the nicest place for villains. Every transfer out of Arkham or Metropolis that went near that place and escaped or tried to escape died. "Hey let me go!"

"C'mon quit struggling. I thought you clowns were supposed to be fearless."

Fighting as the cops pulled her from her cell Harley tried to get back into her cell. "We are when facing heroes because they don't kill! I don't wanna Die!"

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 **Leave a review with what you think of story and Pairing suggestion. Harley is definitely going to be with Naruto. A harem might happen if a girl I think can fit into the story is asked for enough.**


	2. Saving Harleen Quinzel Pt1

Disclaimer: I Do Not Own Naruto Or Dc

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"Hey! Where am I?" Harley yelled. She had been sitting in the same room handcuffed to a metal chair for hours. Which to her immense displeasure was the only thing in the room except her, leaving her with nothing to do but stare at the white walls and the lights overhead. Huffing she pulled on her cuffs twisting her arm to odd angles trying to get free because if she spent another second in this room, she was going to go crazy. Blinking she giggled madly at the thought, she was going to go even crazier.

"Meh, what's so funny Harley?"

"What, who said that." Turning around in her chair Harley saw nothing but another white wall. Frowning at seeing nothing she turned back around jumping a little as a man was standing in front of her. Brow crinkling in concentration she tried to remember if she had seen the person in front of her before. He looked awfully familiar. "Who are you? Some B-man rip off, cause appearing outta nowhere is his thing you know."

Chuckling Naruto crossed his legs levitating a foot off the ground, so he was eye level with Harley. Naruto smiled blue eyes twinkling with delight at how she hadn't immediately started yelling and screaming death threats like he heard she did. Raising his hands in the universal I mean no harm symbol, he waved slightly with his left hand using his right to create a black blank mask. "My name is Naruto Uzumaki, but you might know me better as the New York City Vigilante."

It all clicked for Harley before Naruto even finished his introduction. The levitating and the black mask she had heard about from passing guards in the slammer. Eyes widening as the mask twisted and shrunk into a small black spear she quickly closed her eyes preparing for the pain of being impaled.

Swinging the rod Naruto broke the cuffs holding Harley to the chair. "I'm not here to kill you, the opposite actually. You Harleen have been transferred to New York for rehabilitation."

Raising her hands, she gently rubbed her wrist staring wide-eyed at Naruto. "Rehab... You want me to go to rehab? Well, that's too bad bub because I don't need some hero trying to save me."

"Of course you don't want to be saved. If you did, I wouldn't be needed." Naruto said dropping from his levitation. "But even if you don't want it, I'm still going to save you."

Gaping at the blonde haired vigilante, Harley grinned before smile then breaking out into insane cackles. "Ok blondey, you can save me if you like. I might even reward you."

Not reacting to Harley's flirtatious remark or the heated gaze she was sending his way Naruto smirked grabbing her shoulder. "Good because it wasn't easy getting people to give you this second chance and I don't like going back on my word, so you better behave." Finishing his short speech Naruto flared his Chakra and before Harley could retort the two were pulled into Naruto's Kamui.

(Justice League Headquarters, Hours Earlier)

"Batman you might want to take a look at this." The Flash said getting the dark knight's attention away from the monitors. "The New York Vigilante is back on Tv, and this time it isn't just a report about him."

Gathering around the tv the five Justice members who had been talking about the vigilante days ago watched as the Mayor Of New York City stood next to the vigilante on a stage at time square. Standing tall holding a pure black Shakujo, the same colored swirl mask in place covering his face leaving his blonde hair free to see and dressed in a full-length white kimono the killer vigilante looked more like a priest than a murderer in Bruce's eyes. Narrowing his eyes the bat shook those thoughts away quickly, years in Gotham had taught him looks could be deceiving. "What is he doing Flash?"

"Huh. Oh right, the Mayors Of Gotham and New York signed transfer papers for Harleen Quinzel out of Arkham, to be moved to New York." Flash spoke quickly yet clearly, still focused on the Tv. The speedster didn't know what to think about what was happening in New York. Was the Government tired of Super Villains escaping and decided to send them to New York as a death sentence without getting their hands dirty?

"People of New York, today I stand here with the man who has been a light in our city since his arrival. Crime rates have dropped tremendously and no longer are we defenseless against the Super Villains who decide that our city is their next target. Now our Saviour would like to speak." Stepping aside the Mayor sat in one of the chairs on stage as Naruto took the podium.

"Thank you, Mr. Mayor. Citizens of New York, as many of you, have heard of the rumours of Harleen Quinzel being transferred to New York from Arkham Asylum in Gotham. I am here today to confirm those rumours as true. Harleen Quinzel has been relocated to New York City."

"What! Who would bring that psycho over here?"

"Send her back!"

"Are you going to kill her?"

Tapping his Shakujo on the wooden stage once, Naruto let out a burst of his Chakra, just enough to cause a small gust of wind to blow through the crowd-silencing the shouting. "I understand some of you have your misgivings about the situation, but shouting will not change what is happening. Harleen Quinzel will remain in New York to be rehabilitated as she should have been when she was first arrested."

"What!" Superman exploded as the crowd roared their disapproval. "Is that man insane? He can't be allowed to get away with this."

"Quiet, he is still speaking." Wonderwoman hushed the Kryptonian. "Let us hear what he has to say; then we will plan accordingly."

Unaware of the watchful eyes of the League Naruto tapped the stage, once again silencing the masses. "Many of you have heard what Harleen has done while in Gotham, The laws she has broken, the sins she has committed. What you do not know is how she came to be what she is today. While imprisoned in Arkham the Joker freed himself and tortured Harley, turning her into the monster you know and fear today. If anyone in this crowd would dare to put themselves in her shoes, I will retract my offer and send her back to Arkham. How many of you think you could stay sane after being tortured by Gotham's most ruthless criminal?"

"Why Should we trust what you say is true? We don't even know who you are under that mask."

Locating the speaker, a brown haired, average looking man with a Newspaper badge and camera, Naruto didn't answer motioning for the reporter to continue speaking.

"You heroes hide who you truly are behind masks. You expect us to trust you, why should we? Is trust not a two-way street?" The reporter asked getting yells of agreement from the crowd. "What makes you heroes so special that everyone should put their blind faith in you?"

"Nothing," Naruto answered his voice echoing down the streets as the crowd grew unnaturally quiet at the declaration. "Heroes wear masks to protect their identity not hide them. If the villain's heroes fight to protect you found out who they were under the mask, they will go after that hero's family and friends. But you are correct reporter-san, trust is a two-way street. And if the only way for you to let Harley have a second chance is for you to trust me"-Naruto reached up and unhooked his mask dropping it to the floor revealing his face to the crowd of hundreds in times square and the millions watching on tv at home.-"Then so be it."

"It's him; that's the kid I was talking about. Naruto Uzumaki." Batman explained as the others gave him curious looks at the outraged scowl on his face. "I should have known it was too big a coincidence for him and the vigilante to show up at the same time."

The other League members were in just as much shock seeing the boy they defended days ago reveal himself as the vigilante and a killer. "That boy killed those people. Villains or not, I..." Wonderwoman was at a loss for words as the cheering on the tv grew so loud Superman shut it off.

"It's apparent what we must do. With that stunt and the amount of cheering going on the people will have agreed to let Harley have a second chance. We need to go to New York and talk with the Mayor and this Naruto boy. Neither of them knows the threat Harley poses to their city." Superman said already heading for the exit. He couldn't allow a child to put the life of the citizens of New York into the hands of a serial killer like Harley.

"Superman stop," Batman ordered snapping out of his thoughts. "We should wait till tomorrow to got talk to them. If we go now nothing will be accomplished. The crowd is too excited about the revealing of their heroes identity to listen even if we make a better argument."

(New York Highrise, Present time)

Dropping out of his Kamui dimension Naruto landed on his feet as Harley collapsed on the couch. "It takes some getting used to." He said as Harley got back to her feet still grinning widely.

"Oooh, what fun! Can we go again?" Harley asked sliding up to Naruto's side wrapping herself around his arm. "Why don't you take me somewhere farther away next time?"

Ignoring the question Naruto walked around the apartment the city had given him to use as a home for Harley during her rehabilitation. A large Spacious living room overlooking Central Park connected to an open kitchen. Two doors led to separate bedrooms at the far side, and a third went to a large bathroom which both bedrooms were connected to with doors in the rooms. It was nice, luxurious even, which he was sure was for his benefit more than Harley's comfort. "Your bedroom is the one on the left."

"What if I want the one on the right?" Harley taunted cartwheeling away till she landed back on the couch, sprawling out on the massive leather seats.

"Think of it as your first step out of villain-hood. Generosity!" Naruto called closing the door to his bedroom.

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 **Leave a review with what you think of story and Pairing suggestion. Harley is definitely going to be with Naruto. A harem might happen if a girl I think can fit into the story is asked for enough.**

 **As for Naruto's powers and clothes, yes he has the Rinnegan and Sharingan as well as other powers. No, he will not be OP. In the Naruto world he might have been but in the DC universe, he is not.**


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